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Table 2 Average number of autosomal variants identified per animal using three sequence variant genotyping methods

From: Accurate sequence variant genotyping in cattle using variation-aware genome graphs

 

Full

Filtered

GATK

Graphtyper

SAMtools

GATK

Graphtyper

SAMtools

Total biallelic SNPs

6,324,455

7,384,058

6,617,948

6,105,674

6,533,711

6,564,229

Heterozygous

3,890,351

4,758,297

4,187,882

3,744,336

4,074,011

4,147,033

Homozygous ALT

2,434,104

2,625,761

2,430,066

2,361,338

2,459,700

2,417,196

Ti/Tv

2.17

2.13

2.11

2.20

2.14

2.13

Total biallelic indels

693,697

767,261

1,007,420

691,765

697,637

960,218

Heterozygous

390,495

441,172

616,981

388,622

391,856

593,417

Homozygous ALT

303,202

326,089

390,439

303,143

305,781

366,801

Singletons

49,166

23,406

32,810

41,408

17,999

32,398

  1. The number of variants is presented for the three tools evaluated before (Full) and after (Filtered) applying recommended filters to identify and exclude low quality variants